SLC22A3
Basic information
Region (hg38): 6:160348378-160452577
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (63 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021977.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 62 | 63 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 62 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC22A3 | protein_coding | protein_coding | ENST00000275300 | 11 | 106715 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.77e-10 | 0.695 | 125692 | 0 | 51 | 125743 | 0.000203 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.485 | 279 | 303 | 0.922 | 0.0000166 | 3516 |
Missense in Polyphen | 123 | 133.24 | 0.92317 | 1558 | ||
Synonymous | -0.359 | 126 | 121 | 1.04 | 0.00000675 | 1172 |
Loss of Function | 1.42 | 18 | 25.8 | 0.697 | 0.00000130 | 286 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000293 | 0.000293 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000546 | 0.000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000123 | 0.000123 |
Middle Eastern | 0.000546 | 0.000544 |
South Asian | 0.000523 | 0.000523 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates potential-dependent transport of a variety of organic cations. May play a significant role in the disposition of cationic neurotoxins and neurotransmitters in the brain. {ECO:0000269|PubMed:10196521, ECO:0000269|PubMed:10966924}.;
- Pathway
- Choline metabolism in cancer - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Metformin Pathway, Pharmacokinetics;Sympathetic Nerve Pathway (Neuroeffector Junction);Lamivudine Metabolism Pathway;Synaptic Vesicle Pathway;Tyrosine metabolism;Abacavir transmembrane transport;Abacavir transport and metabolism;Metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Organic cation/anion/zwitterion transport;Histidine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.173
Intolerance Scores
- loftool
- 0.682
- rvis_EVS
- -0.45
- rvis_percentile_EVS
- 24.19
Haploinsufficiency Scores
- pHI
- 0.111
- hipred
- N
- hipred_score
- 0.408
- ghis
- 0.591
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.181
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc22a3
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- drug transmembrane transport;organic cation transport;quaternary ammonium group transport;regulation of appetite;histamine uptake;dopamine uptake;toxin transport
- Cellular component
- plasma membrane;integral component of plasma membrane;membrane
- Molecular function
- dopamine:sodium symporter activity;protein binding;organic cation transmembrane transporter activity;quaternary ammonium group transmembrane transporter activity;toxin transmembrane transporter activity